X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileParse.java;h=69c362ffb5916d7c512df98c3eaa9721e1fb964f;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=051550798cd519fd9fa2a13e35b6946544bc553f;hpb=e601d78bc7762386f570e346a803684c43a66ff1;p=jalview.git
diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 0515507..69c362f 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -1,24 +1,39 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import java.io.*;
-import java.net.*;
+import jalview.util.MessageManager;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.zip.GZIPInputStream;
/**
* implements a random access wrapper around a particular datasource, for
@@ -38,18 +53,22 @@ public class FileParse
// same data source
protected char suffixSeparator = '#';
+
/**
- * character used to write newlines
+ * character used to write newlines
*/
protected String newline = System.getProperty("line.separator");
+
public void setNewlineString(String nl)
{
- newline = nl;
+ newline = nl;
}
+
public String getNewlineString()
{
return newline;
}
+
/**
* '#' separated string tagged on to end of filename or url that was clipped
* off to resolve to valid filename
@@ -86,11 +105,12 @@ public class FileParse
{
if (from == null)
{
- throw new Error(
- "Implementation error. Null FileParse in copy constructor");
+ throw new Error(MessageManager.getString("error.implementation_error_null_fileparse"));
}
if (from == this)
+ {
return;
+ }
index = ++from.index;
inFile = from.inFile;
suffixSeparator = from.suffixSeparator;
@@ -137,18 +157,73 @@ public class FileParse
}
if (!error)
{
+ if (fileStr.toLowerCase().endsWith(".gz"))
+ {
+ try
+ {
+ dataIn = tryAsGzipSource(new FileInputStream(fileStr));
+ dataName = fileStr;
+ return error;
+ } catch (Exception x)
+ {
+ warningMessage = "Failed to resolve as a GZ stream ("
+ + x.getMessage() + ")";
+ // x.printStackTrace();
+ }
+ ;
+ }
+
dataIn = new BufferedReader(new FileReader(fileStr));
dataName = fileStr;
}
return error;
}
+ private BufferedReader tryAsGzipSource(InputStream inputStream)
+ throws Exception
+ {
+ BufferedReader inData = new BufferedReader(new InputStreamReader(
+ new GZIPInputStream(inputStream)));
+ inData.mark(2048);
+ inData.read();
+ inData.reset();
+ return inData;
+ }
+
private boolean checkURLSource(String fileStr) throws IOException,
MalformedURLException
{
errormessage = "URL NOT FOUND";
URL url = new URL(fileStr);
- dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+ //
+ // GZIPInputStream code borrowed from Aquaria (soon to be open sourced) via
+ // Kenny Sabir
+ Exception e = null;
+ if (fileStr.toLowerCase().endsWith(".gz"))
+ {
+ try
+ {
+ InputStream inputStream = url.openStream();
+ dataIn = tryAsGzipSource(inputStream);
+ dataName = fileStr;
+ return false;
+ } catch (Exception ex)
+ {
+ e = ex;
+ }
+ }
+
+ try
+ {
+ dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
+ } catch (IOException q)
+ {
+ if (e != null)
+ {
+ throw new IOException(MessageManager.getString("exception.failed_to_resolve_gzip_stream"), e);
+ }
+ throw q;
+ }
// record URL as name of datasource.
dataName = fileStr;
return false;
@@ -200,14 +275,12 @@ public class FileParse
{
if (checkFileSource(suffixLess))
{
- throw new IOException("Problem opening " + inFile
- + " (also tried " + suffixLess + ") : " + errormessage);
+ throw new IOException(MessageManager.formatMessage("exception.problem_opening_file_also_tried", new String[]{inFile.getName(),suffixLess,errormessage}));
}
}
else
{
- throw new IOException("Problem opening " + inFile + " : "
- + errormessage);
+ throw new IOException(MessageManager.formatMessage("exception.problem_opening_file", new String[]{inFile.getName(),errormessage}));
}
}
}
@@ -219,7 +292,9 @@ public class FileParse
{
checkURLSource(fileStr);
if (suffixSeparator == '#')
+ {
extractSuffix(fileStr); // URL lref is stored for later reference.
+ }
} catch (IOException e)
{
String suffixLess = extractSuffix(fileStr);
@@ -261,7 +336,9 @@ public class FileParse
{
String suffixLess = extractSuffix(fileStr);
if (suffixLess != null)
+ {
is = getClass().getResourceAsStream("/" + suffixLess);
+ }
}
if (is != null)
{
@@ -282,8 +359,7 @@ public class FileParse
if (dataIn == null || error)
{
// pass up the reason why we have no source to read from
- throw new IOException("Failed to read data from source:\n"
- + errormessage);
+ throw new IOException(MessageManager.formatMessage("exception.failed_to_read_data_from_source", new String[]{errormessage}));
}
error = false;
dataIn.mark(READAHEAD_LIMIT);
@@ -303,15 +379,17 @@ public class FileParse
}
else
{
- throw new IOException("Unitialised Source Stream");
+ throw new IOException(MessageManager.getString("exception.no_init_source_stream"));
}
}
public String nextLine() throws IOException
{
if (!error)
+ {
return dataIn.readLine();
- throw new IOException("Invalid Source Stream:" + errormessage);
+ }
+ throw new IOException(MessageManager.formatMessage("exception.invalid_source_stream", new String[]{errormessage}));
}
public boolean isValid()
@@ -343,8 +421,7 @@ public class FileParse
}
else
{
- throw new IOException(
- "Implementation Error: Reset called for invalid source.");
+ throw new IOException(MessageManager.getString("error.implementation_error_reset_called_for_invalid_source"));
}
}
@@ -385,23 +462,27 @@ public class FileParse
{
return dataName;
}
+
/**
* set the (human readable) name or URI for this datasource
+ *
* @param dataname
*/
- protected void setDataName(String dataname) {
+ protected void setDataName(String dataname)
+ {
dataName = dataname;
}
-
/**
* get the underlying bufferedReader for this data source.
+ *
* @return null if no reader available
* @throws IOException
*/
public Reader getReader()
{
- if (dataIn != null) // Probably don't need to test for readiness && dataIn.ready())
+ if (dataIn != null) // Probably don't need to test for readiness &&
+ // dataIn.ready())
{
return dataIn;
}